Sequence-based karyotyping

Abstract

A new method for genomic analysis, termed “Sequence-Based Karyotyping,” is described. Sequence-Based Karyotyping methods for the detection of genomic abnormalities, for diagnosis of hereditary disease, or for diagnosis of spontaneous genomic mutations are also described.

1 . A method of karyotyping a genome of a test cell, comprising: 
 a) obtaining a plurality of test DNA sequences from random locations of the genome of the test cell;    b) mapping said test DNA sequences to a genomic scaffold to obtain a test distribution of mapped sequences to a test region;    c) comparing the test distribution to a reference distribution of obtained from a reference cell;    d) identifying a statistically significant alteration between the test distribution and the reference distribution    wherein if present said alteration indicates a karyotypic difference between the test cell and the reference cell.    
     
     
         2 . The method of  claim 1 , wherein the test and reference distribution are within a contiguous region in the genome.  
     
     
         3 . The method of  claim 1 , wherein the reference distribution comprises a database.  
     
     
         4 . The method of  claim 3 , wherein the database comprises the mapped sequences from a reference genome.  
     
     
         5 . The method of  claim 1 , further comprising prior to step(c): 
 1) obtaining a plurality of reference DNA sequences from random locations of a reference genome of a reference cell and    2) mapping said reference DNA sequences to a genomic scaffold to obtain a reference distribution of reference sequences to a reference region of the genomic scaffold to generate a reference distribution of mapped sequences.    
     
     
         6 . The method of  claim 1  wherein said statistically significant alteration is at confidence level of a p-value of less than 0.05.  
     
     
         7 . The method of  claim 1  wherein said statistically significant alteration is at confidence level of a p-value of less than 0.01.  
     
     
         8 . The method of  claim 1  wherein said statistically significant alteration is at confidence level of a p-value of less than 0.001.  
     
     
         9 . The method of  claim 1  wherein said statistically significant alteration is at confidence level of a p-value of less than 1/24.  
     
     
         10 . The method of  claim 1  wherein said statistically significant alteration is at confidence level of a p-value of less than 1/23.  
     
     
         11 . The method of  claim 1  wherein said statistically significant alteration is at confidence level of a p-value of less than 1/22.  
     
     
         12 . The method of  claim 1  wherein the test cell and the reference cell are of the same species.  
     
     
         13 . The method of  claim 1  wherein said test cell is a eukaryotic cell.  
     
     
         14 . The method of  claim 13 , wherein said eukaryotic cell is a human cell.  
     
     
         15 . The method of  claim 14 , wherein said eukaryotic cell is a cancer cell.  
     
     
         16 . The method of  claim 1  wherein the test cell is a cell from a subject with a hereditary disorder.  
     
     
         17 . The method of  claim 13 , wherein said eukaryotic cell is isolated from amniotic fluid.  
     
     
         18 . The method of  claim 13 , wherein said eukaryotic cell is from an embryo, or a fetus.  
     
     
         19 . The method of  claim 18 , wherein said embryo is derived from in vitro fertilization.  
     
     
         20 . The method of  claim 1 , wherein the test and the reference distribution of mapped sequences comprises more than 1000 mapped sequences.  
     
     
         21 . The method of  claim 1 , wherein the test and the reference distribution of mapped sequences comprises more than 10,000 mapped sequences.  
     
     
         22 . The method of  claim 1 , wherein the test and the reference distribution of mapped sequences comprises more than 100,000 mapped sequences.  
     
     
         23 . The method of  claim 1 , wherein the test region comprises a single chromosome.  
     
     
         24 . The method of  claim 1 , wherein the test region comprise two or more chromosomes.  
     
     
         25 . The method of  claim 2 , wherein the contiguous region is about 4 Mb in length.  
     
     
         26 . The method of  claim 2 , wherein the contiguous region is about 2 Mb in length.  
     
     
         27 . The method of  claim 2 , wherein the contiguous region is 500 kb in length.  
     
     
         28 . The method of  claim 2 , wherein the contiguous region is about 250 kb in length.  
     
     
         29 . The method of  claim 2 , wherein the contiguous region is about 60 kb in length.  
     
     
         30 . The method of  claim 2 , wherein the contiguous region is about 30 kb in length.  
     
     
         31 . The method of  claim 2 , wherein the contiguous region is about 10 kb in length.  
     
     
         32 . The method of  claim 2 , wherein said plurality of test DNA sequences are obtained by: 
 a) providing DNA from a test cell;    b) randomly fragmenting said DNA into a plurality of DNA fragments; and    c) determining the sequence of at least 20 bases from each said DNA fragments.    
     
     
         33 . The method of  claim 32 , wherein the fragmenting is by an enzyme.  
     
     
         34 . The method of or  claim 33 , wherein the enzyme is DNAase 1.  
     
     
         35 . The method of  claim 32 , wherein the fragmenting is by a mechanical method.  
     
     
         36 . The method of  claim 35 , wherein the mechanical method is sonication or nebulization.  
     
     
         37 . The method of  claim 1 , wherein said plurality of DNA fragment comprises at least 1000 DNA fragments.  
     
     
         38 . The method of  claim 1 , wherein said plurality of DNA fragment comprises at least 10,000 DNA fragments.  
     
     
         39 . The method of  claim 1 , wherein said plurality of DNA fragment comprises at least 100,000 DNA fragments.  
     
     
         40 . The method of  claim 1 , wherein said plurality of DNA fragment comprises at least 1,000,000 DNA fragments.  
     
     
         41 . The method of  claim 1 , wherein the mapping step is performed by recording the location and number of occurrences of each of the plurality of DNA sequences.  
     
     
         42 . The method of  claim 1 , wherein a test distribution/reference distribution ratio greater than 1.5 or less than 0.75 is indicative of aneuploidy.  
     
     
         43 . The method of  claim 1 , wherein said test region and reference region is in a sex chromosome, wherein said reference region is from a male cell and said test region is in a female cell, and a test distribution/reference distribution ratio greater than 3.0 or less than 1.5 is indicative of aneuploidy.  
     
     
         44 . The method of  claim 1 , wherein said test region and reference region is in a sex chromosome, wherein said reference region is from a female cell and said test region is in a male cell, and a test distribution/reference distribution ratio greater than 3.0 or less than 1.5 is indicative of aneuploidy.